BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored. RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20 nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68 nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs. CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.